NPASS Compound

Natural Product: NPC608007

The Chemical Classification was calculated by Classyfire, a software for chemical taxonomy calculation. Reference: DOI:10.1186/s13321-016-0174-y.

Chemical Representations

RDKit 3D 85 89 0 0 0 0 0 0 0 0999 V2000 -3.1065 -2.4882 -3.6691 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.0551 -2.6225 -2.6370 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.6975 -3.7743 -2.2468 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.4146 -1.5486 -2.0492 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.4050 -1.6277 -1.0602 C 0 0 1 0 0 0 0 0 0 0 0 0 0.8850 -1.2452 -1.6912 C 0 0 2 0 0 0 0 0 0 0 0 0 1.8023 -0.7907 -0.5339 C 0 0 1 0 0 0 0 0 0 0 0 0 3.1340 -0.8047 -0.8699 O 0 0 0 0 0 0 0 0 0 0 0 0 4.0997 -1.6576 -0.3463 C 0 0 0 0 0 0 0 0 0 0 0 0 3.6879 -2.4813 0.5122 O 0 0 0 0 0 0 0 0 0 0 0 0 5.4935 -1.5994 -0.7656 C 0 0 0 0 0 0 0 0 0 0 0 0 6.4056 -2.4695 -0.2113 C 0 0 0 0 0 0 0 0 0 0 0 0 7.7329 -2.4420 -0.5860 C 0 0 0 0 0 0 0 0 0 0 0 0 8.1878 -1.5444 -1.5256 C 0 0 0 0 0 0 0 0 0 0 0 0 7.2860 -0.6981 -2.0609 N 0 0 0 0 0 0 0 0 0 0 0 0 5.9939 -0.7236 -1.6973 C 0 0 0 0 0 0 0 0 0 0 0 0 1.1796 0.5226 -0.2739 C 0 0 2 0 0 0 0 0 0 0 0 0 0.4743 0.9029 -1.4535 O 0 0 0 0 0 0 0 0 0 0 0 0 0.8516 0.0576 -2.4477 C 0 0 0 0 0 0 0 0 0 0 0 0 2.2202 0.3020 -3.0453 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.0884 -0.0254 -3.6042 C 0 0 0 0 0 0 0 0 0 0 0 0 2.0007 1.6576 0.1214 C 0 0 2 0 0 0 0 0 0 0 0 0 3.4661 1.4698 0.3766 C 0 0 0 0 0 0 0 0 0 0 0 0 1.4748 2.4842 1.2896 C 0 0 0 0 0 0 0 0 0 0 0 0 0.0081 2.6349 1.2947 C 0 0 2 0 0 0 0 0 0 0 0 0 -0.3412 3.1701 2.5810 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.8546 4.4192 2.7847 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.1960 4.9115 4.1506 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.0377 5.1598 1.7845 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.8009 1.4020 0.9857 C 0 0 1 0 0 0 0 0 0 0 0 0 -1.7083 1.7884 -0.0020 O 0 0 0 0 0 0 0 0 0 0 0 0 -3.0646 1.9585 0.2292 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.0409 2.3639 -0.8151 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.4252 1.7362 1.4358 O 0 0 0 0 0 0 0 0 0 0 0 0 0.0301 0.1931 0.7002 C 0 0 2 0 0 0 0 0 0 0 0 0 0.7321 -0.1303 2.0345 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.7856 -0.9851 0.2298 C 0 0 1 0 0 0 0 0 0 0 0 0 -2.1284 -0.9727 0.5377 O 0 0 0 0 0 0 0 0 0 0 0 0 -2.8042 -1.6898 1.4548 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.0566 -2.4396 2.0898 O 0 0 0 0 0 0 0 0 0 0 0 0 -4.2335 -1.6658 1.7453 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.6693 -2.4711 2.7919 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.9883 -2.5552 3.1594 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.9125 -1.8069 2.4562 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.4832 -1.0071 1.4172 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.1657 -0.9410 1.0714 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.6702 -2.4632 -4.6935 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.8420 -3.3111 -3.5541 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.6524 -1.5459 -3.4940 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.2948 -2.7586 -0.9325 H 0 0 0 0 0 0 0 0 0 0 0 0 1.3476 -2.0325 -2.2744 H 0 0 0 0 0 0 0 0 0 0 0 0 1.6228 -1.5732 0.2271 H 0 0 0 0 0 0 0 0 0 0 0 0 6.0556 -3.1794 0.5288 H 0 0 0 0 0 0 0 0 0 0 0 0 8.4751 -3.1169 -0.1647 H 0 0 0 0 0 0 0 0 0 0 0 0 9.2461 -1.5153 -1.8312 H 0 0 0 0 0 0 0 0 0 0 0 0 5.3229 -0.0241 -2.1599 H 0 0 0 0 0 0 0 0 0 0 0 0 2.7390 -0.6821 -3.1614 H 0 0 0 0 0 0 0 0 0 0 0 0 2.1474 0.6679 -4.1169 H 0 0 0 0 0 0 0 0 0 0 0 0 2.8015 1.0719 -2.5487 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.1652 -1.0105 -4.0770 H 0 0 0 0 0 0 0 0 0 0 0 0 0.2578 0.6898 -4.3932 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.0757 0.3690 -3.2909 H 0 0 0 0 0 0 0 0 0 0 0 0 2.0237 2.4221 -0.7303 H 0 0 0 0 0 0 0 0 0 0 0 0 3.8248 2.4898 0.7300 H 0 0 0 0 0 0 0 0 0 0 0 0 3.7609 0.7959 1.1625 H 0 0 0 0 0 0 0 0 0 0 0 0 4.0717 1.3390 -0.5696 H 0 0 0 0 0 0 0 0 0 0 0 0 1.8935 3.5416 1.1698 H 0 0 0 0 0 0 0 0 0 0 0 0 1.9412 2.1932 2.2639 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.2465 3.4746 0.5829 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.7993 4.2284 4.9139 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.7373 5.9173 4.3277 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.3020 4.9502 4.2851 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.3965 1.2138 1.9018 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.0181 2.5150 -0.3037 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.7393 3.3238 -1.2839 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.1381 1.5386 -1.5426 H 0 0 0 0 0 0 0 0 0 0 0 0 0.3943 0.5196 2.8608 H 0 0 0 0 0 0 0 0 0 0 0 0 0.3351 -1.1525 2.3423 H 0 0 0 0 0 0 0 0 0 0 0 0 1.7987 -0.1541 1.9981 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.4526 -1.7890 0.9819 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.9556 -3.0764 3.3687 H 0 0 0 0 0 0 0 0 0 0 0 0 -6.3011 -3.2009 3.9909 H 0 0 0 0 0 0 0 0 0 0 0 0 -7.9494 -1.8692 2.7391 H 0 0 0 0 0 0 0 0 0 0 0 0 -7.2086 -0.4110 0.8560 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.7972 -0.3221 0.2493 H 0 0 0 0 0 0 0 0 0 0 0 0 1 2 1 0 2 3 2 0 2 4 1 0 4 5 1 0 5 6 1 0 6 7 1 0 7 8 1 0 8 9 1 0 9 10 2 0 9 11 1 0 11 12 2 0 12 13 1 0 13 14 2 0 14 15 1 0 15 16 2 0 7 17 1 0 17 18 1 6 18 19 1 0 19 20 1 0 19 21 1 0 17 22 1 0 22 23 1 0 22 24 1 0 24 25 1 0 25 26 1 0 26 27 1 0 27 28 1 0 27 29 2 0 25 30 1 0 30 31 1 0 31 32 1 0 32 33 1 0 32 34 2 0 30 35 1 0 35 36 1 1 35 37 1 0 37 38 1 0 38 39 1 0 39 40 2 0 39 41 1 0 41 42 2 0 42 43 1 0 43 44 2 0 44 45 1 0 45 46 2 0 37 5 1 0 46 41 1 0 19 6 1 0 16 11 1 0 35 17 1 0 1 47 1 0 1 48 1 0 1 49 1 0 5 50 1 1 6 51 1 6 7 52 1 1 12 53 1 0 13 54 1 0 14 55 1 0 16 56 1 0 20 57 1 0 20 58 1 0 20 59 1 0 21 60 1 0 21 61 1 0 21 62 1 0 22 63 1 6 23 64 1 0 23 65 1 0 23 66 1 0 24 67 1 0 24 68 1 0 25 69 1 6 28 70 1 0 28 71 1 0 28 72 1 0 30 73 1 1 33 74 1 0 33 75 1 0 33 76 1 0 36 77 1 0 36 78 1 0 36 79 1 0 37 80 1 1 42 81 1 0 43 82 1 0 44 83 1 0 45 84 1 0 46 85 1 0 M END

Calculated Properties

Physi-Chem Properties

MedChem Properties

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

ADMET: Distribution

ADMET: Metabolism

ADMET: Excretion

ADMET: Toxicity

Species Source

Organism ID	Organism Name	Taxonomy Level	Family	SuperKingdom	Isolation Part	Collection Location	Collection Time	Reference

Note for Reference:
In addition to directly collecting NP source organism data from primary literature (where reference will provided as NCBI PMID or DOI links), NPASS also integrated them from below databases:
☉ UNPD: Universal Natural Products Database [PMID: 23638153].
☉ StreptomeDB: a database of streptomycetes natural products [PMID: 33051671].
☉ TM-MC: a database of medicinal materials and chemical compounds in Northeast Asian traditional medicine [PMID: 26156871].
☉ TCM@Taiwan: a Traditional Chinese Medicine database [PMID: 21253603].
☉ TCMID: a Traditional Chinese Medicine database [PMID: 29106634].
☉ TCMSP: The traditional Chinese medicine systems pharmacology database and analysis platform [PMID: 24735618].
☉ HerDing: a herb recommendation system to treat diseases using genes and chemicals [PMID: 26980517].
☉ MetaboLights: a metabolomics database [PMID: 27010336].
☉ FooDB: a database of constituents, chemistry and biology of food species [www.foodb.ca].

NP Quantity Composition/Concentration

Organism ID	Organism Name	Organism Material Preparation	Organism Part	NP Quantity (Standard)	NP Quantity (Minimum)	NP Quantity (Maximum)	Quantity Unit	Reference

Note for Reference:
In addition to directly collecting NP quantitative data from primary literature (where reference will provided as NCBI PMID or DOI links), NPASS also integrated NP quantitative records for specific NP domains (e.g., NPS from foods or herbs) from domain-specific databases. These databases include:
☉ DUKE: Dr. Duke's Phytochemical and Ethnobotanical Databases.
☉ PHENOL EXPLORER: is the first comprehensive database on polyphenol content in foods [PMID: 24103452], its homepage can be accessed at here.
☉ FooDB: a database of constituents, chemistry and biology of food species [www.foodb.ca].

Biological Activity

Molecular-level activity

Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference

In vitro activity

Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference

In vivo activity

Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference

Experimental ADME

Experiment Model	Experiment Tissue	ADME Type	ADME Relation	ADME Value	ADME Unit	Reference

Experimental Toxicity

Quantitative toxicity

Experiment Model	Experiment Organism	Toxicity Type	Toxicity Relation	Toxicity Value	Toxicity Unit	Reference

Common Abbreviations:
LC: Lethal Concentration; LD: Lethal Dose; LT:Lethal Time; NOAEL: No-observed-adverse-effect Level; BMDL: Benchmark Dose Lower Confidence Limit; BMD: Benchmark Dose; BMC:Benchmark Concentration; LOAEL: Lowest Observed Adverse Effect Level; RfD:Reference Dose; RfC:Reference Concentration; MRL: Minimal Risk Level; MEG: Maximum Exposure Guideline; PAC: Protective Action Criteria

Categorical toxicity labels

Hepatotoxicity	Carcinogenicity	Mutagenicity	Cardiotoxicity	Respiratory Toxicity	Eye Irritation	Endocrine Disruption

Note for Reference:
In addition to directly collecting NP quantitative data from primary literature (where reference will provided as NCBI PMID or DOI links), NPASS also integrated NP toxicity records from domain-specific databases. These databases include:
☉ ToxValDB: a curated database that compiles quantitative toxicity values for chemicals from diverse public sources to support toxicological research and risk assessment.
☉ TOXRIC: a comprehensive, free-to-access, online database providing toxicological/feature data. The toxicity labels are retrieved from this database. [PMID: 36400569]

Chemically structural similarity

Similar Active Natural Products in NPASS

Top-200 similar NPs were calculated against the active-NP-set (includes approximately 50,000 NPs with experimentally-derived bioactivity available in NPASS)

Similarity is measured using the Tanimoto coefficient (Tc) , which compares the binary fingerprints of two molecules. Tc is calculated as the intersection divided by the union of '1' bits in the fingerprints, ranging from 0 to 1, with 1 indicating highest similarity.

● The left chart: Distribution of similarity level between NPC608007 and all remaining natural products in the NPASS database.
● The right table: Most similar natural products (Tc>=0.5 or Top200).

range	Tanimoto Coefficient
0-0.1	21855
0.1-0.2	26297
0.2-0.3	1252
0.3-0.4	275
0.4-0.5	119
0.5-0.6	41
0.6-0.7	10
0.7-0.8	0
0.8-0.85	2
0.85-0.9	0
0.9-0.95	0
0.95-1	0

Similarity Score	Similarity Level	Natural Product ID
0.8472	Intermediate Similarity	NPC483887
0.8472	Intermediate Similarity	NPC158020
0.7632	Intermediate Similarity	NPC212768
0.7632	Intermediate Similarity	NPC4421
0.7536	Intermediate Similarity	NPC481047
0.7536	Intermediate Similarity	NPC481045
0.6538	Remote Similarity	NPC609924
0.6506	Remote Similarity	NPC301368
0.6506	Remote Similarity	NPC84815
0.65	Remote Similarity	NPC609221
0.6386	Remote Similarity	NPC610927
0.6296	Remote Similarity	NPC481050
0.6118	Remote Similarity	NPC473089
0.6049	Remote Similarity	NPC481071
0.6047	Remote Similarity	NPC75600
0.6047	Remote Similarity	NPC483884
0.5897	Remote Similarity	NPC473060
0.5862	Remote Similarity	NPC473115
0.5789	Remote Similarity	NPC200592
0.5789	Remote Similarity	NPC610542
0.575	Remote Similarity	NPC147217
0.5625	Remote Similarity	NPC147880
0.5584	Remote Similarity	NPC195647
0.5581	Remote Similarity	NPC14499
0.5556	Remote Similarity	NPC148062
0.5517	Remote Similarity	NPC483889
0.5517	Remote Similarity	NPC488900
0.5513	Remote Similarity	NPC66761
0.5513	Remote Similarity	NPC483843
0.5513	Remote Similarity	NPC476094
0.5412	Remote Similarity	NPC36021
0.5385	Remote Similarity	NPC270498
0.5349	Remote Similarity	NPC481068
0.5326	Remote Similarity	NPC30171
0.5281	Remote Similarity	NPC483881
0.5269	Remote Similarity	NPC479046
0.5227	Remote Similarity	NPC88593
0.519	Remote Similarity	NPC473081
0.5185	Remote Similarity	NPC483862
0.5181	Remote Similarity	NPC137718
0.5176	Remote Similarity	NPC479043
0.5169	Remote Similarity	NPC488899
0.5169	Remote Similarity	NPC481069
0.5165	Remote Similarity	NPC483864
0.5165	Remote Similarity	NPC127026
0.5165	Remote Similarity	NPC483890
0.5125	Remote Similarity	NPC475429
0.5125	Remote Similarity	NPC211137
0.5122	Remote Similarity	NPC51314
0.5122	Remote Similarity	NPC483886
0.5106	Remote Similarity	NPC483885
0.5104	Remote Similarity	NPC488902
0.5104	Remote Similarity	NPC488903
0.506	Remote Similarity	NPC163719
0.506	Remote Similarity	NPC95810
0.5055	Remote Similarity	NPC56953
0.5055	Remote Similarity	NPC6576

Similar Clinical/Approved Drugs

Similarity level is defined by Tanimoto coefficient (Tc) between two molecules.

● The left chart: Distribution of similarity level between NPC608007 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.5 or Top200).

range	Tanimoto Coefficient
0-0.1	4000
0.1-0.2	5028
0.2-0.3	119
0.3-0.4	3
0.4-0.5	0
0.5-0.6	0
0.6-0.7	0
0.7-0.8	0
0.8-0.85	0
0.85-0.9	0
0.9-0.95	0
0.95-1	0

Similarity Score	Similarity Level	Drug ID	Developmental Stage
		NPD

Bioactivity similarity

Similar Natural Products in NPASS

Similarity level is defined by Bioactivity similarity was calculated based on bioactivity descriptors of compounds. The bioactivity descriptors were calculated by a recently developed AI algorithm Chemical Checker (CC) [Nature Biotechnology, 38:1087–1096, 2020; Nature Communications, 12:3932, 2021], which evaluated bioactivity similarities at five levels:
☉ A: chemistry similarity;
☉ B: biological targets similarity;
☉ C: networks similarity;
☉ D: cell-based bioactivity similarity;
☉ E: similarity based on clinical data.
Those 5 categories of CC bioactivity descriptors were calculated and then subjected to manifold projection using UMAP algorithm, to project all NPs on a 2-Dimensional space. The current NP was highlighted with a small circle in the 2-D map. Below figures: left-to-right, A-to-E.

A: chemistry similarity

B: biological targets similarity

C: networks similarity

D: cell-based bioactivity similarity

E: similarity based on clinical data